This is what the quest for a unifying theory is all about. Einstein came up with a theory that explained much about the very large, which didn't explain the physics of the very small, and then spent his later years trying to come up with a theory that explained it all and failed. And others have followed... and failed.
A unifying theory would be nice I suppose, but I'm not certain why it's important. The Theory of Relativity explains a lot, but it doesn't explain everything, even if we take quantum mechanics out of the picture completely. And no one seems upset about that.
The very small just doesn't act like the very large, but they do mesh. The theories may not mesh, but the reality seems to work fine on a practical level. Maybe someday we will understand, but I can't know that for sure.